SAXSdb — 9p3n

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	9p3n
沉积日期 deposition_date	2025-06-14
结构标题 title	The open state of zebrafish TRPM5 with 1mM EDTA and 0.5mM CBTA
关键词 keywords	TRPM5 channel; ion channel; cation channel; sodium channel; calcium; CBTA, TRANSPORT PROTEIN; TRANSPORT PROTEIN
实验方法 method	ELECTRON MICROSCOPY

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2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	51.39 Å
回转半径 Rg (电子) rg_electron	50.92 Å
零角强度 I(0) i0	4888150000.00
分子量 molecular_weight	402090.0 kDa
排除体积 excluded_volume	396230 Å³
包络体积 envelope_volume	801700 Å³
水化壳体积 shell_volume	125070 Å³
包络直径 envelope_diameter	159.0 Å
壳层 Rg shell_rg	60.18 Å
包络 Rg envelope_rg	48.99 Å
形状 Rg shape_rg	50.93 Å
总 Rg total_rg	51.10 Å
总原子数 total_atoms	30588
残基数 n_residues	3984
球谐函数阶数 n_harmonics	20
q 范围 q_range	— – 0.5000 Å⁻¹
数据点数 n_points	101
壳层类型 shell_type	directional
溶剂电子密度 solvent_density	0.3340 e/Å³
壳层衬度 contrast_shell	0.0300 e/Å³
CRYSOL 版本 crysol_version	4.1.3

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3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	154.2 Å
Rg (实空间) rg_real	51.08 Å
Rg 误差 (实空间) rg_real_error	1.21 Å
I(0) (实空间) i0_real	4.8880e+09
I(0) 误差 (实空间) i0_real_error	8.7110e+07
Rg (倒空间) rg_reciprocal	51.64 Å
I(0) (倒空间) i0_reciprocal	4892000000.0000
解质量估计 total_estimate	0.8794
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	69.6 Å
偏度 Skewness skewness	0.011
峰度 Kurtosis kurtosis	-0.522
角度范围 angular_range	— – 0.1550 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	291000000.0000
实空间数据点数 n_real_points	32
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.920; Stabil: 0.996; Sysdev: 1.000; Positv: 1.000; Valcen: 0.945; Smooth: 0.733

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4. 晶体学与实验 4. Crystallography & Experiment

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5. 实体与聚合体信息 (5)

Entity 1 polymer

描述 description	Green fluorescent protein,Transient receptor potential cation channel subfamily M member 5
分子量 formula_weight	166815.7 kDa
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,D,B,C
原子数 atom_count	30588

MHHHHHHHHAAASAWSHPQFEKGGGSGGGSGGSAWSHPQFEKGGGSGGGSGGMVSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSKLSKDPNEKRDHMVLLEFVTAAGITLGMDELYKSGLRSGLVPRGSGGRATMVEKSSERFDKQMAGRLGDIDFTGVSRTRGKFVRVTSSTDPAEIYQILTKQWGLAPPHLVVALMGGDEVAQLKPWLRDTLRKGLVKAAQSTGAWILTSGLRFGITKNLGQAVRDHSLASTSPKVRVVAIGIAPWNMIQNRDLLLSAKPDHPATYPTEDLPYGAVYSLDCNHSHFILVDEDPKRPGATGEMRVKMLKHISLQRTGYGGTGSIEIPVLCLLVHGEPRILQKMYKNIQNSIPWLILAGSGGVADILVTLMDRGCWDADIVQELLINTFPDGLHSTEITSWTKLIQRILDHGHLLTVHDPEQDSELDTVILKALVKACKSQSQEAQDFLDELKLAVAWNRVDIAKSEIFSGDVQWSAQDLEEVMMEALVNDKPDFVRLFVDNGVNIKQFLTYGRLQELYCSVSEKNLLHTLLLKKNQERQAQLARKRMSGNPNNELGDRKFRFTFHEVSKVLKDFLDDTCKGFYQKLPAERMGKGRLFHSQKNLPDMDRRCEHPWRDLFLWAILQNRQEMANYFWAMGPEAVAAALVGCKIMKEMAHLATEAESARSMKNAKYEQFAMDLFSECYSNSEDRAYSLLVRKTCCWSKATVLNIATLAEAKCFFAHDGVQALLTKVWWGAMRTDTSISRLVLTFFIPPLVWTSLIKFNPEEQVSKDEGEPFAELDSLETEQALLLTDGDPVAGEGSAETAARSCSATFIRVVLRRWNRFWSAPVTVFMGNVIMYFAFLILFSYVLLLDFRPPPPYGPSAAEIILYFWVFTLVLEEIRQSFFTDEDMSILKKMKLYVEDNWNKCDMVAISLFVVGLSCRMAMSTYEAGRTVLALDFMVFTLRLIHIFAIHKQLGPKIIIVERMIKDVFFFLFFLSVWLIAYGVTTQALLHPNDPRIDWVFRRALYRPYLHIFGQIPLEEIDAAKMPDDNCTTDVQEIILGTLPPCPNIYANWLVILLLVIYLLVTNVLLLNLLIAMFSYTFQVVQENADIFWKFQRYNLIVEYHSRPALAPPFIIISHITQALLSFIKKTENTQDLLERELPSGLDQKLMTWETVQKENYLAKLEHEHRESSGERLRYTSSKVQTLLRMVGGFKDQEKRMATVETEVRYCGEVLSWIAECFHKSTLKCDRDAPKAPRSIAGSSRDQQPQGAKRQQPGGHPAYGTDKKLPFIDHFE

来源 Source

来源生物 organism	Danio rerio
通用名 common_name	zebrafish
NCBI 分类编号 ncbi_taxonomy_id	7955
宿主生物 host_organism	Homo sapiens

Entity 2 non-polymer

描述 description	CALCIUM ION
分子量 formula_weight	40.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 3 non-polymer

描述 description	;(2R)-2-(hydroxymethyl)-4-{[(25R)-10alpha,14beta,17beta-spirost-5-en-3beta-yl]oxy}butyl 4-O-alpha-D-glucopyranosyl-beta-D-glucopyranoside ;
分子量 formula_weight	841.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 4 non-polymer

描述 description	(25R)-14beta,17beta-spirost-5-en-3beta-ol
分子量 formula_weight	414.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 5 non-polymer

描述 description	5-chloro-N-[(5-chloro-1,3-thiazol-2-yl)methyl]-1,2-benzothiazol-6-amine
分子量 formula_weight	316.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

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7. 引用文献 (1)

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分辨率 resolution	3.50 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	5426

fit	/app/data/saxs_computation/p3/9p3n/9p3n.fit
pddf	/app/data/pr_computation/p3/9p3n/9p3n.pr.out
profile	/app/data/saxs_computation/p3/9p3n/9p3n.dat

The open state of zebrafish TRPM5 with 1mM EDTA and 0.5mM CBTA

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution